diff --git a/interactive-mining-angular-frontend b/interactive-mining-angular-frontend
new file mode 160000
index 0000000..1300909
--- /dev/null
+++ b/interactive-mining-angular-frontend
@@ -0,0 +1 @@
+Subproject commit 1300909bca20fa744bde85d3f44fda559f43eb93
diff --git a/interactive-mining-madoap/madoap/.gitignore b/interactive-mining-backend/madoap/.gitignore
similarity index 100%
rename from interactive-mining-madoap/madoap/.gitignore
rename to interactive-mining-backend/madoap/.gitignore
diff --git a/interactive-mining-backend/madoap/src/.idea/modules.xml b/interactive-mining-backend/madoap/src/.idea/modules.xml
new file mode 100644
index 0000000..f669a0e
--- /dev/null
+++ b/interactive-mining-backend/madoap/src/.idea/modules.xml
@@ -0,0 +1,8 @@
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/interactive-mining-backend/madoap/src/.idea/src.iml b/interactive-mining-backend/madoap/src/.idea/src.iml
new file mode 100644
index 0000000..24643cc
--- /dev/null
+++ b/interactive-mining-backend/madoap/src/.idea/src.iml
@@ -0,0 +1,12 @@
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/interactive-mining-backend/madoap/src/.idea/workspace.xml b/interactive-mining-backend/madoap/src/.idea/workspace.xml
new file mode 100644
index 0000000..d8761a5
--- /dev/null
+++ b/interactive-mining-backend/madoap/src/.idea/workspace.xml
@@ -0,0 +1,161 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ true
+ DEFINITION_ORDER
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1 Code loaded! Please make sure that you separate each code with newline!".format(fname)
+ else:
+ data['data'] = codes
+ data['respond'] = "{0} Codes loaded successfully!".format(len(lines))
+ self.set_secure_cookie('madgikmining_grantsuploaded', str(len(lines)))
+ self.write(json.dumps(data))
+ self.finish()
+ except Exception as ints:
+ self.set_status(400)
+ self.write("A server error occurred, please contact administrator!")
+ self.finish()
+ print ints
+ return
+
+
+class UpdateConceptsHandler(BaseHandler):
+ passwordless=True
+ def set_default_headers(self):
+ self.set_header("Access-Control-Allow-Origin", "http://localhost:4200")
+ self.set_header("Access-Control-Allow-Headers", "Origin, X-Requested-With, Content-Type, Accept")
+ self.set_header('Access-Control-Allow-Methods', 'POST, OPTIONS')
+ self.set_header('Access-Control-Allow-Credentials', 'true')
+ self.set_header('Content-Type', 'application/json')
+ def options(self):
+ # no body
+ self.set_status(204)
+ self.finish()
+ def post(self):
+ try:
+ # get user id from cookie. Must have
+ user_id = self.get_secure_cookie('madgikmining')
+ if user_id is None:
+ self.set_status(400)
+ self.write("Missing cookie containing user's id...")
+ return
+ # get data
+ concepts = json.loads(json.loads(self.request.body)['concepts'])
+ # write data to physical file
+ cname = "/tmp/p{0}.tsv".format(user_id)
+ fh = open(cname, 'w')
+ concepts_len = 0
+ for key, value in concepts.iteritems():
+ if key == '':
+ continue
+ concepts_len += 1
+ fh.write("{0}\t{1}\n".format(key,value))
+ fh.close()
+ # data to be sent
+ data = {}
+ if concepts_len == 0:
+ self.set_status(400)
+ self.write("You have to provide at least one concept to continue!")
+ return
+ else:
+ data['respond'] = "{0} Codes loaded successfully!".format(concepts_len)
+ self.set_secure_cookie('madgikmining_grantsuploaded', str(concepts_len))
+ self.write(json.dumps(data))
+ self.finish()
+ except Exception as ints:
+ self.set_status(400)
+ self.write("A server error occurred, please contact administrator!")
+ self.finish()
+ print ints
+ return
+
+
+class GetDocSamplesHandler(BaseHandler):
+ passwordless=True
+ def set_default_headers(self):
+ self.set_header("Access-Control-Allow-Origin", "http://localhost:4200")
+ self.set_header("Access-Control-Allow-Headers", "Origin, X-Requested-With, Content-Type, Accept")
+ self.set_header('Access-Control-Allow-Methods', 'GET, OPTIONS')
+ self.set_header('Access-Control-Allow-Credentials', 'true')
+ self.set_header('Content-Type', 'application/json')
+ def options(self):
+ # no body
+ self.set_status(204)
+ self.finish()
+ def get(self):
+ try:
+ # get user id from cookie. Must have
+ user_id = self.get_secure_cookie('madgikmining')
+ if user_id is None:
+ self.set_status(400)
+ self.write("Missing cookie containing user's id...")
+ return
+ data = {}
+ doc_samples = []
+ doc_samples.append({'name': 'Egi', 'documents': 104})
+ doc_samples.append({'name': 'Fbi', 'documents': 1023})
+ doc_samples.append({'name': 'NSF', 'documents': 140})
+ doc_samples.append({'name': 'Swiss', 'documents': 502})
+ doc_samples.append({'name': 'Egi', 'documents': 104})
+ doc_samples.append({'name': 'Fbi', 'documents': 1023})
+ doc_samples.append({'name': 'NSF', 'documents': 140})
+ doc_samples.append({'name': 'Swiss', 'documents': 502})
+ doc_samples.append({'name': 'Egi', 'documents': 104})
+ doc_samples.append({'name': 'Fbi', 'documents': 1023})
+ doc_samples.append({'name': 'NSF', 'documents': 140})
+ doc_samples.append({'name': 'Swiss', 'documents': 502})
+ doc_samples.append({'name': 'Egi', 'documents': 104})
+ doc_samples.append({'name': 'Fbi', 'documents': 1023})
+ doc_samples.append({'name': 'NSF', 'documents': 140})
+ doc_samples.append({'name': 'Swiss', 'documents': 502})
+ data['documents'] = doc_samples
+ self.write(json.dumps(data))
+ self.finish()
+ except Exception as ints:
+ self.set_status(400)
+ self.write("A server error occurred, please contact administrator!")
+ self.finish()
+ print ints
+ return
+
+
+class UploadDocumentsHandler(BaseHandler):
+ passwordless=True
+ def set_default_headers(self):
+ self.set_header("Access-Control-Allow-Origin", "http://localhost:4200")
+ self.set_header("Access-Control-Allow-Headers", "Origin, X-Requested-With, Content-Type, Accept")
+ self.set_header('Access-Control-Allow-Methods', 'POST, OPTIONS')
+ self.set_header('Access-Control-Allow-Credentials', 'true')
+ self.set_header('Content-Type', 'application/json')
+ def options(self):
+ # no body
+ self.set_status(204)
+ self.finish()
+ def post(self):
+ try:
+ # get user id from cookie. Must have
+ user_id = self.get_secure_cookie('madgikmining')
+ if user_id is None:
+ self.set_status(400)
+ self.write("Missing cookie containing user's id...")
+ return
+ fileinfo = self.request.files['upload'][0]
+ fname = fileinfo['filename']
+ extn = os.path.splitext(fname)[1]
+ # data to be sent
+ data = {}
+ # must be .pdf, .txt or .json
+ if extn != ".pdf" and extn != ".txt" and extn != ".json":
+ self.set_status(400)
+ self.write("File must be .pdf, .json or .txt")
+ return
+ return
+ # write data to physical file
+ cname = "/tmp/docs{0}{1}".format(user_id, extn)
+ fh = open(cname, 'w')
+ fh.write(fileinfo['body'])
+ fh.close()
+ # Convert pdf to txt and then to json format
+ if extn == ".pdf":
+ import subprocess as sub
+ p = sub.Popen(['pdftotext', '-enc', 'UTF-8', cname],stdout=sub.PIPE,stderr=sub.PIPE)
+ output, errors = p.communicate()
+ if errors:
+ self.set_status(400)
+ self.write("An error occurred when trying to convert .pdf to .txt...")
+ return
+ os.remove(cname)
+ cname = "/tmp/docs{0}.txt".format(user_id)
+ with open(cname, 'r') as fin:
+ docData=fin.read().replace('\n', ' ')
+ if len(docData)==0:
+ self.set_status(400)
+ self.write("An error occurred when trying to convert .pdf to text...")
+ return
+ with open("/tmp/docs{0}.json".format(user_id), "wb") as fout:
+ json.dump({"text":docData,"id":os.path.splitext(fname)[0]}, fout)
+ os.remove(cname)
+ # else check if txt is in correct json format
+ elif extn == ".txt" or extn == ".json":
+ try:
+ jsonlist = []
+ for line in open(cname, 'r'):
+ jsonlist.append(json.loads(line))
+ os.rename(cname, "/tmp/docs{0}.json".format(user_id))
+ except ValueError, e:
+ self.set_status(400)
+ self.write("File is not in a valid json format...")
+ os.remove(cname)
+ print e
+ return
+ file_name = "/tmp/docs%s.json" % (user_id)
+ if os.path.isfile(file_name):
+ lines = sum(1 for line in open(file_name))
+ data['respond'] = "{0} Documents loaded successfully!".format(lines)
+ data['data'] = lines
+ self.write(json.dumps(data))
+ self.finish()
+ except Exception as ints:
+ self.set_status(400)
+ self.write("A server error occurred, please contact administrator!")
+ self.finish()
+ print ints
+ return
+
+
+class ChooseDocSampleHandler(BaseHandler):
+ passwordless=True
+ def set_default_headers(self):
+ self.set_header("Access-Control-Allow-Origin", "http://localhost:4200")
+ self.set_header("Access-Control-Allow-Headers", "Origin, X-Requested-With, Content-Type, Accept")
+ self.set_header('Access-Control-Allow-Methods', 'POST, OPTIONS')
+ self.set_header('Access-Control-Allow-Credentials', 'true')
+ self.set_header('Content-Type', 'application/json')
+ def options(self):
+ # no body
+ self.set_status(204)
+ self.finish()
+ def post(self):
+ try:
+ # get user id from cookie. Must have
+ user_id = self.get_secure_cookie('madgikmining')
+ if user_id is None:
+ self.set_status(400)
+ self.write("Missing cookie containing user's id...")
+ return
+ doc_sample = json.loads(self.request.body)['docsample']
+ if doc_sample == '':
+ self.set_status(400)
+ self.write("A doc sample name must be provided")
+ return
+ sample_file_name = ""
+ if doc_sample == "Egi":
+ sample_file_name = "static/egi_sample.tsv"
+ elif doc_sample == "Rcuk":
+ sample_file_name = "static/rcuk_sample.tsv"
+ elif doc_sample == "Arxiv":
+ sample_file_name = "static/arxiv_sample.tsv"
+ else:
+ self.set_status(400)
+ self.write("No Doc sample with this name")
+ return
+ sample_file = open(sample_file_name, 'r')
+ # write data to physical file
+ cname = "/tmp/docs{0}.json".format(user_id)
+ fh = open(cname, 'w')
+ while 1:
+ copy_buffer = sample_file.read(1048576)
+ if not copy_buffer:
+ break
+ fh.write(copy_buffer)
+ fh.close()
+ lines_num = sum(1 for line in open(cname))
+
+ # data to be sent
+ data = {}
+ if lines_num == 0:
+ self.set_status(400)
+ self.write("File must contain atleast one document...")
+ return
+ else:
+ data['respond'] = "{0} Documents loaded successfully!".format(lines_num)
+ data['data'] = lines_num
+ self.write(json.dumps(data))
+ self.finish()
+ except Exception as ints:
+ self.set_status(400)
+ self.write("A server error occurred, please contact administrator!")
+ self.finish()
+ print ints
+ return
+
+
+class AlreadyDocumentsHandler(BaseHandler):
+ passwordless=True
+ def set_default_headers(self):
+ self.set_header("Access-Control-Allow-Origin", "http://localhost:4200")
+ self.set_header("Access-Control-Allow-Headers", "Origin, X-Requested-With, Content-Type, Accept")
+ self.set_header('Access-Control-Allow-Methods', 'GET, OPTIONS')
+ self.set_header('Access-Control-Allow-Credentials', 'true')
+ self.set_header('Content-Type', 'application/json')
+ def options(self):
+ # no body
+ self.set_status(204)
+ self.finish()
+ def get(self):
+ try:
+ # get user id from cookie. Must have
+ user_id = self.get_secure_cookie('madgikmining')
+ if user_id is None:
+ self.set_status(400)
+ self.write("Missing cookie containing user's id...")
+ return
+ data = {}
+ if msettings.RESET_FIELDS == 1:
+ data['data'] = -1
+ else:
+ data['data'] = 0
+ file_name = "/tmp/docs%s.json" % (user_id)
+ if os.path.isfile(file_name):
+ data['data'] = sum(1 for line in open(file_name))
+ msettings.RESET_FIELDS = 0
+ self.write(json.dumps(data))
+ self.finish()
+ except Exception as ints:
+ self.set_status(400)
+ self.write("A server error occurred, please contact administrator!")
+ self.finish()
+ print ints
+ return
+
+
+class RunMiningHandler(BaseHandler):
+ passwordless=True
+ def set_default_headers(self):
+ self.set_header("Access-Control-Allow-Origin", "http://localhost:4200")
+ self.set_header("Access-Control-Allow-Headers", "Origin, X-Requested-With, Content-Type, Accept")
+ self.set_header('Access-Control-Allow-Methods', 'POST, OPTIONS')
+ self.set_header('Access-Control-Allow-Credentials', 'true')
+ self.set_header('Content-Type', 'application/json')
+ def options(self):
+ # no body
+ self.set_status(204)
+ self.finish()
+ def post(self):
+ try:
+ # get user id from cookie. Must have
+ user_id = self.get_secure_cookie('madgikmining')
+ if user_id is None:
+ self.set_status(400)
+ self.write("Missing cookie containing user's id...")
+ return
+ request_arguments = json.loads(self.request.body)
+ # get the database cursor
+ cursor=msettings.Connection.cursor()
+ # data to be sent
+ data = {}
+ # set the textwindow size
+ extracontextprev = 10
+ extracontextnext = 10
+ contextprev = 10
+ contextnext = 5
+ # Automatically find middle size from grant codes white spaces
+ querygrantsize = "select max(p1) from (select regexpcountwords('\s',stripchars(p1)) as p1 from (setschema 'p1,p2' file '/tmp/p{0}.tsv' dialect:tsv))".format(user_id)
+ contextmiddle = [r for r in cursor.execute(querygrantsize)][0][0]+1
+ if 'contextprev' in request_arguments and request_arguments['contextprev'] != '':
+ contextprev = int(request_arguments['contextprev'])
+ if contextprev < 0 or contextprev > 20:
+ self.set_status(400)
+ self.write("Context size must be in its limits...")
+ return
+ if 'contextnext' in request_arguments and request_arguments['contextnext'] != '':
+ contextnext = int(request_arguments['contextnext'])
+ if contextnext < 0 or contextnext > 20:
+ self.set_status(400)
+ self.write("Context size must be in its limits...")
+ return
+ j2sextraprev = "j2s(prev1"
+ for cnt in xrange(2,extracontextprev+1):
+ j2sextraprev += ",prev"+str(cnt)
+ j2sextraprev += ")"
+ j2sprev = ""
+ j2scontext = "("
+ if contextprev:
+ j2scontext = "j2s(prev"+str(extracontextprev+1)
+ j2sprev = "j2s(prev"+str(extracontextprev+1)
+ for cnt in xrange(extracontextprev+2,extracontextprev+contextprev+1):
+ j2sprev += ",prev"+str(cnt)
+ j2scontext += ",prev"+str(cnt)
+ j2sprev += ")"
+ j2scontext += ","
+ else:
+ j2scontext = "j2s("
+ j2snext = "j2s(next1"
+ j2scontext += "middle"
+ if contextnext:
+ j2scontext += ",next1"
+ for cnt in xrange(2,contextnext+1):
+ j2snext += ",next"+str(cnt)
+ j2scontext += ",next"+str(cnt)
+ j2snext += ")"
+ j2scontext += ")"
+ j2sextranext = "j2s(next"+str(contextnext+1)
+ for cnt in xrange(contextnext+2,extracontextnext+contextnext+1):
+ j2sextranext += ",next"+str(cnt)
+ j2sextranext += ")"
+ print j2sextraprev, j2sprev, j2snext, j2sextranext, j2scontext
+
+ # create positive and negative words weighted regex text
+ pos_set = neg_set = conf = whr_conf = ''
+ if 'poswords' in request_arguments and request_arguments['poswords'] != '{}':
+ data['poswords'] = []
+ # construct math string for positive words matching calculation with weights
+ pos_words = json.loads(request_arguments['poswords'])
+ for key, value in pos_words.iteritems():
+ # MONO GIA TO EGI
+ pos_set += r'regexpcountuniquematches("%s",%s)*%s + ' % (key,j2scontext,value)
+ # ORIGINAL
+ # pos_set += r'regexpcountuniquematches("(?:\b)%s(?:\b)",j2s(prev,middle,next))*%s + ' % (key,value)
+ data['poswords'].append(key)
+ pos_set += "0"
+ if 'negwords' in request_arguments and request_arguments['negwords'] != '{}':
+ data['negwords'] = []
+ # construct math string for negative words matching calculation with weights
+ neg_words = json.loads(request_arguments['negwords'])
+ for key, value in neg_words.iteritems():
+ # MONO GIA TO EGI
+ neg_set += r'regexpcountuniquematches("%s",%s)*%s + ' % (key,j2scontext,value)
+ # ORIGINAL
+ # neg_set += r'regexpcountuniquematches("(?:\b)%s(?:\b)",j2s(prev,middle,next))*%s - ' % (key,value)
+ data['negwords'].append(key)
+ neg_set += "0"
+ if pos_set != '' and neg_set != '':
+ conf = ", ({0} - {1})".format(pos_set, neg_set)
+ elif pos_set != '':
+ conf = ", {0}".format(pos_set)
+ elif neg_set != '':
+ conf = ", -{0}".format(neg_set)
+ if conf != '':
+ conf += ' as conf'
+ whr_conf = 'and conf>=0'
+
+ if numberOfDocsUploaded(user_id) != 0:
+ doc_filters = "comprspaces(regexpr('[\n|\r]',d2,' '))"
+ ackn_filters = "comprspaces(regexpr(\"\\'\", p2,''))"
+ if 'punctuation' in request_arguments and request_arguments['punctuation'] == "1":
+ doc_filters = 'keywords('+doc_filters+')'
+ ackn_filters = 'keywords('+ackn_filters+')'
+ if 'lettercase' in request_arguments and request_arguments['lettercase'] != '' and request_arguments['lettercase'] != 'none':
+ if request_arguments['lettercase'] == 'lowercase':
+ doc_filters = 'lower('+doc_filters+')'
+ ackn_filters = 'lower('+ackn_filters+')'
+ elif request_arguments['lettercase'] == 'uppercase':
+ doc_filters = 'upper('+doc_filters+')'
+ ackn_filters = 'upper('+ackn_filters+')'
+ if 'stopwords' in request_arguments and request_arguments['stopwords'] == "1":
+ doc_filters = 'filterstopwords('+doc_filters+')'
+ ackn_filters = 'filterstopwords('+ackn_filters+')'
+ print "DOCCC", doc_filters
+ list(cursor.execute("drop table if exists grantstemp"+user_id, parse=False))
+ query_pre_grants = "create temp table grantstemp{0} as select stripchars(p1) as gt1, case when p2 is null then null else {1} end as gt2 from (setschema 'p1,p2' file '/tmp/p{0}.tsv' dialect:tsv)".format(user_id, ackn_filters)
+ cursor.execute(query_pre_grants)
+ list(cursor.execute("drop table if exists docs"+user_id, parse=False))
+ query1 = "create temp table docs{0} as select d1, {1} as d2 from (setschema 'd1,d2' select jsonpath(c1, '$.id', '$.text') from (file '/tmp/docs{0}.json'))".format(user_id, doc_filters)
+ cursor.execute(query1)
+ else:
+ self.set_status(400)
+ self.write("You have to provide atleast 1 document...")
+ return
+
+ list(cursor.execute("drop table if exists grants"+user_id, parse=False))
+ # string concatenation workaround because of the special characters conflicts
+ if 'wordssplitnum' in request_arguments and request_arguments['wordssplitnum'] != '':
+ words_split = int(request_arguments['wordssplitnum'])
+ # MONO GIA TO EGI
+ if 0 < words_split and words_split <= 10:
+ acknowledgment_split = r'textwindow2s(gt2,0,'+str(words_split)+r',0)'
+ else:
+ acknowledgment_split = r'"dummy" as prev, gt2 as middle, "dummy" as next'
+ # ORIGINAL
+ # if 0 < words_split and words_split <= 10:
+ # acknowledgment_split = r'textwindow2s(regexpr("([\-\[\]\/\{\}\(\)\*\+\?\.\\\^\$\|])", gt2, "\\\1"),0,'+str(words_split)+r',0)'
+ # else:
+ # acknowledgment_split = r'"dummy" as prev, regexpr("([\-\[\]\/\{\}\(\)\*\+\?\.\\\^\$\|])", gt2, "\\\1") as middle, "dummy" as next'
+
+ # query0 = r"create temp table grants"+user_id+r' as select gt1 as g1, jmergeregexp(jgroup("(?<=[\s\b])"||middle||"(?=[\s\b])")) as g2 from '+r"(setschema 'gt1,prev,middle,next' select gt1, "+acknowledgment_split+r' from grantstemp'+user_id+r' where (gt1 or gt1!="") and gt2 not null) group by gt1 union all select distinct gt1 as g1, "(?!.*)" as g2 from grantstemp'+user_id+r" where (gt1 or gt1!='') and gt2 is null"
+ query0 = r"create temp table grants"+user_id+r' as select gt1 as g1, jmergeregexp(jgroup(middle)) as g2 from '+r"(setschema 'gt1,prev,middle,next' select gt1, "+acknowledgment_split+r' from grantstemp'+user_id+r' where (gt1 or gt1!="") and gt2 != "") group by gt1 union all select distinct gt1 as g1, "(?!.*)" as g2 from grantstemp'+user_id+r" where (gt1 or gt1!='') and gt2 = ''"
+ cursor.execute(query0)
+ query0get = "select * from grants{0}".format(user_id)
+ results0get = [r for r in cursor.execute(query0get)]
+ print results0get
+
+ # FOR EGI ONLY
+ query2 = r'select distinct d1, g1, extraprev, prev, middle, next, extranext, acknmatch, max(confidence) as confidence from (select d1, g1, regexpcountuniquematches(g2, '+j2scontext+r') as confidence, stripchars('+j2sextraprev+r') as extraprev, stripchars('+j2sprev+r') as prev, middle, stripchars('+j2snext+r') as next, stripchars('+j2sextranext+r') as extranext, '+j2scontext+r' as context, regexprfindall(g2, '+j2scontext+r') as acknmatch '+conf+r' from (select d1, textwindow(d2,'+str(extracontextprev+contextprev)+r','+str(extracontextnext+contextnext)+r','+str(contextmiddle)+r') from docs'+user_id+r'), (select g1, g2 from grants'+user_id+r') T where regexprmatches("(\b|\d|\W)"||T.g1||"(\b|\d|\W)",middle) '+whr_conf+r') group by d1'
+ # ORIGINAL
+ # query2 = "select d1, g1, context, acknmatch, max(confidence) as confidence from (select d1, g1, regexpcountuniquematches(g2, j2s(prev,middle,next)) as confidence, j2s(prev,middle,next) as context, regexprfindall(g2, j2s(prev,middle,next)) as acknmatch {0} from (select d1, textwindow2s(d2,20,{3},20) from docs{1}), (select g1, g2 from grants{1}) T where regexprmatches(T.g1,middle) {2}) group by d1".format(conf, user_id, whr_conf, contextmiddle)
+
+ # OLD ONE
+ # query2 = "select c1, c3 {0} from (select c1, textwindow2s(c2,10,1,5) from (select * from docs{1})), (select c3 from grants{1}) T where middle = T.c3 {2}".format(conf, user_id, whr_conf)
+ results = [r for r in cursor.execute(query2)]
+ print results
+ doctitles = {}
+ for r in results:
+ if r[0] not in doctitles:
+ doctitles[r[0]] = []
+ doctitles[r[0]].append({"match": r[1], "extraprev": r[2], "prev": r[3], "middle": r[4], "next":r[5], "extranext":r[6], "acknmatch": json.loads(r[7]), "confidence": r[8]})
+ data['matches'] = doctitles
+ data['respond'] = "Matching results updated!"
+ self.write(json.dumps(data))
+ self.flush()
+ self.finish()
+ except Exception as ints:
+ self.set_status(400)
+ self.write("A server error occurred, please contact administrator!")
+ self.finish()
+ print ints
+ return
+
+
+class PrepareSavedProfileHandler(BaseHandler):
+ passwordless=True
+ def set_default_headers(self):
+ self.set_header("Access-Control-Allow-Origin", "http://localhost:4200")
+ self.set_header("Access-Control-Allow-Headers", "Origin, X-Requested-With, Content-Type, Accept")
+ self.set_header('Access-Control-Allow-Methods', 'POST, OPTIONS')
+ self.set_header('Access-Control-Allow-Credentials', 'true')
+ self.set_header('Content-Type', 'application/json')
+ def options(self):
+ # no body
+ self.set_status(204)
+ self.finish()
+ def post(self):
+ try:
+ # get user id from cookie. Must have
+ user_id = self.get_secure_cookie('madgikmining')
+ if user_id is None:
+ self.set_status(400)
+ self.write("Missing cookie containing user's id...")
+ return
+ import sys
+ sys.path.append(msettings.MADIS_PATH)
+ import madis
+ # get the database cursor
+ # profile file name
+ profile_file_name = "/tmp/OAMiningProfile_{0}.oamp".format(user_id)
+ cursor=madis.functions.Connection(profile_file_name).cursor()
+ # Create poswords table
+ cursor.execute("drop table if exists poswords", parse=False)
+ cursor.execute("create table poswords(c1,c2)", parse=False)
+ # Create negwords table
+ cursor.execute("drop table if exists negwords", parse=False)
+ cursor.execute("create table negwords(c1,c2)", parse=False)
+ # Create filters table
+ cursor.execute("drop table if exists filters", parse=False)
+ cursor.execute("create table filters(c1,c2)", parse=False)
+ # Create grants table
+ cursor.execute("drop table if exists grants", parse=False)
+ cursor.execute("create table grants(c1,c2)", parse=False)
+ request_arguments = json.loads(self.request.body)
+ if 'poswords' in request_arguments and request_arguments['poswords'] != '{}':
+ # construct math string for positive words matching calculation with weights
+ pos_words = json.loads(request_arguments['poswords'])
+ cursor.executemany("insert into poswords(c1,c2) values(?,?)",
+ (
+ (key, value,) for key, value in pos_words.iteritems()
+ )
+ )
+ if 'negwords' in request_arguments and request_arguments['negwords'] != '{}':
+ # construct math string for negative words matching calculation with weights
+ neg_words = json.loads(request_arguments['negwords'])
+ cursor.executemany("insert into negwords(c1,c2) values(?,?)",
+ (
+ (key, value,) for key, value in neg_words.iteritems()
+ )
+ )
+ if 'filters' in request_arguments and request_arguments['filters'] != '{}':
+ # construct math string for negative words matching calculation with weights
+ filters = json.loads(request_arguments['filters'])
+ cursor.executemany("insert into filters(c1,c2) values(?,?)",
+ (
+ (key, value,) for key, value in filters.iteritems()
+ )
+ )
+ if numberOfGrantsUploaded(user_id, self.get_secure_cookie('madgikmining_grantsuploaded')) != 0:
+ cursor.execute("insert into grants select stripchars(c1) as c1, stripchars(c2) as c2 from (file '/tmp/p{0}.tsv')".format(user_id))
+ cursor.close()
+
+ data = {}
+ data['data'] = 1
+ self.write(json.dumps(data))
+ self.flush()
+ self.finish()
+ except Exception as ints:
+ self.set_status(400)
+ self.write("A server error occurred, please contact administrator!")
+ self.finish()
+ print ints
+ return
+
+
+class SaveProfileToDatabaseHandler(BaseHandler):
+ passwordless=True
+ def set_default_headers(self):
+ self.set_header("Access-Control-Allow-Origin", "http://localhost:4200")
+ self.set_header("Access-Control-Allow-Headers", "Origin, X-Requested-With, Content-Type, Accept")
+ self.set_header('Access-Control-Allow-Methods', 'POST, OPTIONS')
+ self.set_header('Access-Control-Allow-Credentials', 'true')
+ self.set_header('Content-Type', 'application/json')
+ def options(self):
+ # no body
+ self.set_status(204)
+ self.finish()
+ def post(self):
+ try:
+ # get user id from cookie. Must have
+ user_id = self.get_secure_cookie('madgikmining')
+ if user_id is None:
+ self.set_status(400)
+ self.write("Missing cookie containing user's id...")
+ return
+ # get data
+ profile_id = json.loads(self.request.body)['id']
+ profile_name = json.loads(self.request.body)['name']
+ doc_name = json.loads(self.request.body)['docname']
+ docs_number = json.loads(self.request.body)['docsnumber']
+ # copy profile file to a unique user profile file
+ profile_file_name = "/tmp/OAMiningProfile_{0}.oamp".format(user_id)
+ # check if profile has already an id
+ old_profile = True
+ if profile_id == '':
+ # get unique profile id
+ profile_id = getNewProfileId()
+ old_profile = False
+ unique_profile_file_name = "/tmp/OAMiningProfile_{0}_{1}.oamp".format(user_id,profile_id)
+ copyfile(profile_file_name, unique_profile_file_name)
+ # copy profile docs to unique profile docs
+ if doc_name != '' and docs_number != 0:
+ docs_file_name = "/tmp/docs{0}.json".format(user_id)
+ unique_docs_file_name = "/tmp/OAMiningDocs_{0}_{1}.json".format(user_id,profile_id)
+ copyfile(docs_file_name, unique_docs_file_name)
+ # write new profile to database
+ import sys
+ sys.path.append(msettings.MADIS_PATH)
+ import madis
+ # database file name
+ database_file_name = "/tmp/OAMiningProfilesDatabase_{0}.db".format(user_id)
+ # get the database cursor
+ cursor=madis.functions.Connection(database_file_name).cursor()
+ user_profiles = []
+ if old_profile:
+ query = 'UPDATE database set name="{1}", datecreated="{2}", status="{3}", matches="{4}", docname="{5}", docsnumber="{6}" where id="{0}"'.format(profile_id,profile_name,"24-03-2018","Ready","8/8",doc_name,docs_number)
+ else:
+ query = 'INSERT INTO database VALUES("{0}","{1}","{2}","{3}","{4}","{5}","{6}")'.format(profile_id,profile_name,"24-03-2018","Ready","8/8",doc_name,docs_number)
+ cursor.execute(query, parse=False)
+ cursor.close()
+ self.write(json.dumps({}))
+ self.finish()
+ except Exception as ints:
+ self.set_status(400)
+ self.write("A server error occurred, please contact administrator!")
+ self.finish()
+ print ints
+ return
+
+
+class DownloadProfileHandler(BaseHandler):
+ passwordless=True
+ def set_default_headers(self):
+ self.set_header("Access-Control-Allow-Origin", "http://localhost:4200")
+ self.set_header("Access-Control-Allow-Headers", "Origin, X-Requested-With, Content-Type, Accept")
+ self.set_header('Access-Control-Allow-Methods', 'POST, OPTIONS')
+ self.set_header('Access-Control-Allow-Credentials', 'true')
+ self.set_header('Content-Type', 'application/oamp')
+ def options(self):
+ # no body
+ self.set_status(204)
+ self.finish()
+ def post(self):
+ try:
+ # get user id from cookie. Must have
+ user_id = self.get_secure_cookie('madgikmining')
+ if user_id is None:
+ self.set_status(400)
+ self.write("Missing cookie containing user's id...")
+ return
+ profile_id = json.loads(self.request.body)['id']
+ unique_profile_file_name = "/tmp/OAMiningProfile_{0}_{1}.oamp".format(user_id,profile_id)
+ buf_size = 4096
+ self.set_header('Content-Type', 'application/octet-stream')
+ self.set_header('Content-Disposition', 'attachment; filename=' + "OAMiningProfile_{0}_{1}.oamp".format(user_id,profile_id))
+ self.flush()
+ with open(unique_profile_file_name, 'r') as f:
+ while True:
+ data = f.read(buf_size)
+ if not data:
+ break
+ self.write(data)
+ self.finish()
+ except Exception as ints:
+ self.set_status(400)
+ self.write("A server error occurred, please contact administrator!")
+ self.finish()
+ print ints
+ return
+
+
+class madAppHandler(BaseHandler):
+ def get(self):
+ try:
+ appname=re.match(r'.+/([^/]+)/?$', self.request.uri).groups()[0].lower()
+ except AttributeError:
+ raise tornado.web.HTTPError(404)
+
+ appobj=None
+ for ap in madapps.apps:
+ if ap['link']==appname:
+ appobj=ap
+ break
+
+ if appobj==None:
+ raise tornado.web.HTTPError(404)
+
+ self.render('madappview.html', app=appobj, apps=filteredapps, evals=filteredevals, settings=msettings)
+
+class madAppDataHandler(BaseHandler):
+
+ @tornado.web.asynchronous
+ def post(self):
+ try:
+ appname, queryname=[x.lower() for x in re.match(r'.+/([^/]+)/(.+)$', self.request.uri).groups()]
+ except AttributeError:
+ raise tornado.web.HTTPError(404)
+
+ appobj=None
+ query=''
+ for ap in madapps.apps:
+ if ap['link']==appname:
+ if queryname in ap:
+ appobj=ap
+ if queryname=='query':
+ query=appobj['query']
+ else:
+ query=appobj[queryname]['query']
+ break
+
+ if appobj==None:
+ raise tornado.web.HTTPError(404)
+
+ params=dict(((x.replace(' ','_'),y[0].replace('\n','')) for x,y in self.request.arguments.iteritems()) )
+ self.executequery(query, params)
+
+
+
+
+def main():
+ global filteredapps, filteredevals
+
+ def getqtext(query,params):
+ query=query.strip('\n \s')
+ query=escape.xhtml_escape(query)
+ for i in params:
+ i=i.replace(' ','_')
+ query=re.sub(':'+i, ''+escape.xhtml_escape(i)+'', query)
+ query=re.sub('$'+i, ''+escape.xhtml_escape(i)+'', query)
+ query=re.sub('@'+i, ''+escape.xhtml_escape(i)+'', query)
+ return query.replace("\n","
")
+
+ if 'initial_queries' in queries:
+ try:
+ list(msettings.Connection.cursor().execute(queries['initial_queries']))
+ except Exception, e:
+ raise Exception("Error when executing DB_INITIAL_EXECUTE:\n"+queries['initial_queries']+"\nThe error was:\n"+ str(e))
+
+ tornado.options.parse_command_line()
+
+ logging.info('Completed madApp startup scripts')
+
+ filteredapps=filter(lambda x:("eval" not in x),madapps.apps)
+ filteredevals=filter(lambda x:("eval" in x),madapps.apps)
+
+ if not msettings.DEBUG:
+ sockets = tornado.netutil.bind_sockets(options.port)
+ tornado.process.fork_processes(0)
+ server = tornado.httpserver.HTTPServer(Application())
+ # ssl_options = {
+ #"certfile": os.path.join("/home/openaire/ssl/certificate.crt"),
+ #"keyfile": os.path.join("/home/openaire/ssl/privateKey.key"),
+#})
+ server.add_sockets(sockets)
+ tornado.ioloop.IOLoop.instance().start()
+ else:
+# debug case
+ http_server = tornado.httpserver.HTTPServer(Application())
+ http_server.bind(options.port)
+ http_server.start(1)
+ tornado.ioloop.IOLoop.instance().start()
+
+
+
+if __name__ == "__main__":
+ main()
diff --git a/interactive-mining-madoap/madoap/src/settings.py b/interactive-mining-backend/madoap/src/settings.py
similarity index 100%
rename from interactive-mining-madoap/madoap/src/settings.py
rename to interactive-mining-backend/madoap/src/settings.py
diff --git a/interactive-mining-madoap/madoap/src/static/BG_Footer_2.jpg b/interactive-mining-backend/madoap/src/static/BG_Footer_2.jpg
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/BG_Footer_2.jpg
rename to interactive-mining-backend/madoap/src/static/BG_Footer_2.jpg
diff --git a/interactive-mining-madoap/madoap/src/static/OA CONNECT_A.png b/interactive-mining-backend/madoap/src/static/OA CONNECT_A.png
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/OA CONNECT_A.png
rename to interactive-mining-backend/madoap/src/static/OA CONNECT_A.png
diff --git a/interactive-mining-madoap/madoap/src/static/OA CONNECT_B.png b/interactive-mining-backend/madoap/src/static/OA CONNECT_B.png
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/OA CONNECT_B.png
rename to interactive-mining-backend/madoap/src/static/OA CONNECT_B.png
diff --git a/interactive-mining-madoap/madoap/src/static/OA DISCOVER_A.png b/interactive-mining-backend/madoap/src/static/OA DISCOVER_A.png
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/OA DISCOVER_A.png
rename to interactive-mining-backend/madoap/src/static/OA DISCOVER_A.png
diff --git a/interactive-mining-madoap/madoap/src/static/OA DISCOVER_B.png b/interactive-mining-backend/madoap/src/static/OA DISCOVER_B.png
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/OA DISCOVER_B.png
rename to interactive-mining-backend/madoap/src/static/OA DISCOVER_B.png
diff --git a/interactive-mining-madoap/madoap/src/static/OpenAIREplus_logo.png b/interactive-mining-backend/madoap/src/static/OpenAIREplus_logo.png
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/OpenAIREplus_logo.png
rename to interactive-mining-backend/madoap/src/static/OpenAIREplus_logo.png
diff --git a/interactive-mining-madoap/madoap/src/static/OpenAIREplus_logo1.png b/interactive-mining-backend/madoap/src/static/OpenAIREplus_logo1.png
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/OpenAIREplus_logo1.png
rename to interactive-mining-backend/madoap/src/static/OpenAIREplus_logo1.png
diff --git a/interactive-mining-madoap/madoap/src/static/OpenAIREplus_logo2.png b/interactive-mining-backend/madoap/src/static/OpenAIREplus_logo2.png
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/OpenAIREplus_logo2.png
rename to interactive-mining-backend/madoap/src/static/OpenAIREplus_logo2.png
diff --git a/interactive-mining-madoap/madoap/src/static/ResizeSensor.js b/interactive-mining-backend/madoap/src/static/ResizeSensor.js
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/ResizeSensor.js
rename to interactive-mining-backend/madoap/src/static/ResizeSensor.js
diff --git a/interactive-mining-madoap/madoap/src/static/accessURL.js b/interactive-mining-backend/madoap/src/static/accessURL.js
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/accessURL.js
rename to interactive-mining-backend/madoap/src/static/accessURL.js
diff --git a/interactive-mining-madoap/madoap/src/static/ajax-loader.gif b/interactive-mining-backend/madoap/src/static/ajax-loader.gif
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/ajax-loader.gif
rename to interactive-mining-backend/madoap/src/static/ajax-loader.gif
diff --git a/interactive-mining-madoap/madoap/src/static/animations.css b/interactive-mining-backend/madoap/src/static/animations.css
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/animations.css
rename to interactive-mining-backend/madoap/src/static/animations.css
diff --git a/interactive-mining-madoap/madoap/src/static/comments.css b/interactive-mining-backend/madoap/src/static/comments.css
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/comments.css
rename to interactive-mining-backend/madoap/src/static/comments.css
diff --git a/interactive-mining-madoap/madoap/src/static/configure-profile.js b/interactive-mining-backend/madoap/src/static/configure-profile.js
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/configure-profile.js
rename to interactive-mining-backend/madoap/src/static/configure-profile.js
diff --git a/interactive-mining-madoap/madoap/src/static/create-upload-profile.js b/interactive-mining-backend/madoap/src/static/create-upload-profile.js
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/create-upload-profile.js
rename to interactive-mining-backend/madoap/src/static/create-upload-profile.js
diff --git a/interactive-mining-madoap/madoap/src/static/custom.css b/interactive-mining-backend/madoap/src/static/custom.css
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/custom.css
rename to interactive-mining-backend/madoap/src/static/custom.css
diff --git a/interactive-mining-madoap/madoap/src/static/database.db b/interactive-mining-backend/madoap/src/static/database.db
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/database.db
rename to interactive-mining-backend/madoap/src/static/database.db
diff --git a/interactive-mining-madoap/madoap/src/static/dl119_files/80x15.png b/interactive-mining-backend/madoap/src/static/dl119_files/80x15.png
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/dl119_files/80x15.png
rename to interactive-mining-backend/madoap/src/static/dl119_files/80x15.png
diff --git a/interactive-mining-madoap/madoap/src/static/dl119_files/Home-icon.png b/interactive-mining-backend/madoap/src/static/dl119_files/Home-icon.png
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/dl119_files/Home-icon.png
rename to interactive-mining-backend/madoap/src/static/dl119_files/Home-icon.png
diff --git a/interactive-mining-madoap/madoap/src/static/dl119_files/Logo_Horizontal_white_small.png b/interactive-mining-backend/madoap/src/static/dl119_files/Logo_Horizontal_white_small.png
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/dl119_files/Logo_Horizontal_white_small.png
rename to interactive-mining-backend/madoap/src/static/dl119_files/Logo_Horizontal_white_small.png
diff --git a/interactive-mining-madoap/madoap/src/static/dl119_files/custom.css b/interactive-mining-backend/madoap/src/static/dl119_files/custom.css
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/dl119_files/custom.css
rename to interactive-mining-backend/madoap/src/static/dl119_files/custom.css
diff --git a/interactive-mining-madoap/madoap/src/static/dl119_files/ec_logo_inv_small.png b/interactive-mining-backend/madoap/src/static/dl119_files/ec_logo_inv_small.png
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/dl119_files/ec_logo_inv_small.png
rename to interactive-mining-backend/madoap/src/static/dl119_files/ec_logo_inv_small.png
diff --git a/interactive-mining-madoap/madoap/src/static/dl119_files/theme.css b/interactive-mining-backend/madoap/src/static/dl119_files/theme.css
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/dl119_files/theme.css
rename to interactive-mining-backend/madoap/src/static/dl119_files/theme.css
diff --git a/interactive-mining-madoap/madoap/src/static/dl119_files/uikit-icons-max.js b/interactive-mining-backend/madoap/src/static/dl119_files/uikit-icons-max.js
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/dl119_files/uikit-icons-max.js
rename to interactive-mining-backend/madoap/src/static/dl119_files/uikit-icons-max.js
diff --git a/interactive-mining-madoap/madoap/src/static/dl119_files/uikit.css b/interactive-mining-backend/madoap/src/static/dl119_files/uikit.css
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/dl119_files/uikit.css
rename to interactive-mining-backend/madoap/src/static/dl119_files/uikit.css
diff --git a/interactive-mining-madoap/madoap/src/static/dl119_files/uikit.js b/interactive-mining-backend/madoap/src/static/dl119_files/uikit.js
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/dl119_files/uikit.js
rename to interactive-mining-backend/madoap/src/static/dl119_files/uikit.js
diff --git a/interactive-mining-madoap/madoap/src/static/egi_sample.tsv b/interactive-mining-backend/madoap/src/static/egi_sample.tsv
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/egi_sample.tsv
rename to interactive-mining-backend/madoap/src/static/egi_sample.tsv
diff --git a/interactive-mining-madoap/madoap/src/static/error-handling.js b/interactive-mining-backend/madoap/src/static/error-handling.js
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/error-handling.js
rename to interactive-mining-backend/madoap/src/static/error-handling.js
diff --git a/interactive-mining-madoap/madoap/src/static/exampleDocs.txt b/interactive-mining-backend/madoap/src/static/exampleDocs.txt
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/exampleDocs.txt
rename to interactive-mining-backend/madoap/src/static/exampleDocs.txt
diff --git a/interactive-mining-madoap/madoap/src/static/exampleProfile.oamp b/interactive-mining-backend/madoap/src/static/exampleProfile.oamp
similarity index 96%
rename from interactive-mining-madoap/madoap/src/static/exampleProfile.oamp
rename to interactive-mining-backend/madoap/src/static/exampleProfile.oamp
index e57f5fe..a2c0b58 100644
Binary files a/interactive-mining-madoap/madoap/src/static/exampleProfile.oamp and b/interactive-mining-backend/madoap/src/static/exampleProfile.oamp differ
diff --git a/interactive-mining-madoap/madoap/src/static/favicon.ico b/interactive-mining-backend/madoap/src/static/favicon.ico
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/favicon.ico
rename to interactive-mining-backend/madoap/src/static/favicon.ico
diff --git a/interactive-mining-madoap/madoap/src/static/fp7grants.csv b/interactive-mining-backend/madoap/src/static/fp7grants.csv
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/fp7grants.csv
rename to interactive-mining-backend/madoap/src/static/fp7grants.csv
diff --git a/interactive-mining-madoap/madoap/src/static/interactivemining.js b/interactive-mining-backend/madoap/src/static/interactivemining.js
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/interactivemining.js
rename to interactive-mining-backend/madoap/src/static/interactivemining.js
diff --git a/interactive-mining-madoap/madoap/src/static/interactiveminingExample.txt b/interactive-mining-backend/madoap/src/static/interactiveminingExample.txt
similarity index 100%
rename from interactive-mining-madoap/madoap/src/static/interactiveminingExample.txt
rename to interactive-mining-backend/madoap/src/static/interactiveminingExample.txt
diff --git a/interactive-mining-madoap/madoap/src/static/interactivemining_styles.css b/interactive-mining-backend/madoap/src/static/interactivemining_styles.css
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